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Table 8 Identification of conserved regulatory motifs from catfish untranslated regions (UTRs)

From: Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote

Regulatory motifs

Standard name

Location (UTR)

Number of UTRs

IRE

Iron Responsive Element

5' and 3’

13

IRES

Internal Ribosome Entry Site

5'

2,491

SXL_BS

SXL binding site

5' and 3’

1,469

TOP

Terminal Oligopyrimidine Tract

5'

265

UNR-bs

UNR binding site

5' and 3’

907

uORF

Upstream Open Reading Frame

5'

5,492

15-LOX-DICE

15-Lipoxygenase Differentiation Control Element

3'

2

ADH_DRE

Alcohol dehydrogenase 3'UTR downregulation control element

3'

91

ARE2

AU-rich class-2 Element

3'

82

BRD-BOX

Brd-Box

3'

578

BRE

Bruno 3'UTR responsive element

3'

28

CPE

Cytoplasmic polyadenylation element

3'

180

G3A

Elastin G3A 3'UTR stability motif

3'

2

GLUT1

Glusose transporter type-1 3'UTR cis-acting element

3'

2

GY-BOX

GY-Box

3'

232

INS_SCE

Insulin 3'UTR stability element

3'

1

K-BOX

K-Box

3'

919

MBE

Musashi binding element

3'

3,546

SECIS1

Selenocysteine Insertion Sequence - type 1

3'

42

SECIS2

Selenocysteine Insertion Sequence - type 2

3'

36

TGE

TGE translational regulation element

3'

5

  1. Catfish conserved regulatory motifs were identified by comparison with experimentally validated regulatory motifs deposited in UTRsite database using pattern search program UTRscan. Number of UTRs denotes the number of catfish UTRs from which the corresponding regulatory motifs were identified.